scispace - formally typeset
Search or ask a question
Journal ArticleDOI

A Cartesian grid embedded boundary method for the heat equation on irregular domains

13 Nov 2001-Journal of Computational Physics (Academic Press Professional, Inc.)-Vol. 173, Iss: 2, pp 620-635
TL;DR: An algorithm for solving the heat equation on irregular time-dependent domains is presented, based on the Cartesian grid embedded boundary algorithm of Johansen and Colella, combined with a second-order accurate discretization of the time derivative.
About: This article is published in Journal of Computational Physics.The article was published on 2001-11-13 and is currently open access. It has received 161 citations till now. The article focuses on the topics: Mixed boundary condition & Boundary (topology).

Summary (1 min read)

Jump to: [1. INTRODUCTION] and [FIG. 1.]

1. INTRODUCTION

  • For the time discretization, for the fixed-boundary problem the authors use either the Crank-Nicolson method or the method of Twizell, Gumel and Arigu (TGA) [10] .
  • The authors algorithm is stable and achieves second-order accuracy both on problems with fixed domain and on problems with a time-dependent domain (t) with boundaries moving with constant velocities.

FIG. 1.

  • Centers of cells in (t old ) are shown with solid circles, and centers of cells in (tnew) -(t old ) are shown with unfilled circles.
  • The authors solve (19) numerically on a rectangular domain with three elliptically-shaped holes, with boundary conditions computed using the exact solution (18).
  • In the moving-boundary problem, the holes move with constant velocities.
  • With both fixed and moving boundaries, the authors solve two separate problems with different boundary conditions: Dirichlet conditions on all boundaries; Dirichlet conditions on the fixed external boundaries, but Neumann conditions on the boundaries of the ellipses.

Did you find this useful? Give us your feedback

Figures (15)
Citations
More filters
Journal ArticleDOI
TL;DR: In this article, a method for representing curved boundaries for the solution of the Navier-Stokes equations on a non-uniform, staggered, three-dimensional Cartesian grid is presented.

206 citations


Cites background from "A Cartesian grid embedded boundary ..."

  • ...[22] to the solution of the timedependent heat equation....

    [...]

Journal ArticleDOI
TL;DR: A second-order Godunov algorithm to solve time-dependent hyperbolic systems of conservation laws on irregular domains by hybridizing the authors' conservative discretization with a stable, nonconservative discretized at irregular control volumes, and redistributing the difference in the mass increments to nearby cells in a way that preserves stability and local conservation.

202 citations


Cites methods from "A Cartesian grid embedded boundary ..."

  • ...A second application would be to combine this algorithm with the finite-volume algorithms for elliptic and parabolic problems in [8,9,15] to solve incompressible or low-Mach number flow problems with irregular fixed or free boundaries, following the ideas in [1]....

    [...]

Journal ArticleDOI
TL;DR: A parameter estimation method for reaction-diffusion tumor growth models using time series of medical images and it is shown that several parameters can be uniquely identified in the case of fixing one parameter, namely the proliferation rate of tumor cells.
Abstract: Reaction-diffusion based tumor growth models have been widely used in the literature for modeling the growth of brain gliomas. Lately, recent models have started integrating medical images in their formulation. Including different tissue types, geometry of the brain and the directions of white matter fiber tracts improved the spatial accuracy of reaction-diffusion models. The adaptation of the general model to the specific patient cases on the other hand has not been studied thoroughly yet. In this paper, we address this adaptation. We propose a parameter estimation method for reaction-diffusion tumor growth models using time series of medical images. This method estimates the patient specific parameters of the model using the images of the patient taken at successive time instances. The proposed method formulates the evolution of the tumor delineation visible in the images based on the reaction-diffusion dynamics; therefore, it remains consistent with the information available. We perform thorough analysis of the method using synthetic tumors and show important couplings between parameters of the reaction-diffusion model. We show that several parameters can be uniquely identified in the case of fixing one parameter, namely the proliferation rate of tumor cells. Moreover, regardless of the value the proliferation rate is fixed to, the speed of growth of the tumor can be estimated in terms of the model parameters with accuracy. We also show that using the model-based speed, we can simulate the evolution of the tumor for the specific patient case. Finally, we apply our method to two real cases and show promising preliminary results.

197 citations


Cites methods from "A Cartesian grid embedded boundary ..."

  • ...The numerical scheme for the PDE [47] uses linear interpolation of the diffusion tensors between voxels creating higher diffusion within the grey matter neighboring white matter....

    [...]

  • ...The first one is the difference between numerical schemes we use to solve the reaction-diffusion PDE and the traveling time formulation....

    [...]

  • ...In [28], Hogea et al. propose a PDE based method where they invert their model equations and solve a constrained PDE optimization problem to estimate the parameters....

    [...]

  • ...Their formulation consists of reaction-diffusion type partial differential equations (PDEs) with the reaction term [first term in (1)] representing the proliferation and the diffusion term representing the infiltration [21]....

    [...]

  • ...This correction scheme makes sure that as we solve the (5) we follow the characteristic directions of the PDE [53]....

    [...]

Journal ArticleDOI
TL;DR: A two-dimensional model of transcription, translation, and nuclear membrane transport in eukaryotic cells is presented to demonstrate the feasibility of the Gillespie method in studying cell-wide biological processes.
Abstract: A method is developed for incorporating diffusion of chemicals in complex geometries into stochastic chemical kinetics simulations. Systems are modeled using the reaction-diffusion master equation, with jump rates for diffusive motion between mesh cells calculated from the discretization weights of an embedded boundary method. Since diffusive jumps between cells are treated as first order reactions, individual realizations of the stochastic process can be created by the Gillespie method. Numerical convergence results for the underlying embedded boundary method, and for the stochastic reaction-diffusion method, are presented in two dimensions. A two-dimensional model of transcription, translation, and nuclear membrane transport in eukaryotic cells is presented to demonstrate the feasibility of the method in studying cell-wide biological processes.

162 citations


Cites background or methods from "A Cartesian grid embedded boundary ..."

  • ...For comparison to our discretization, note that in [21] (Fk)i± 12 ek is chosen to be the standard centered difference approximation when the kth face does not intersect a boundary....

    [...]

  • ...The time integration was performed using the second order, L0 stable, implicit Runge– Kutta method mentioned in [21]....

    [...]

  • ...For faces cut by the boundary, [21] interpolates between the centered difference flux in neighboring cells to approximate the flux at the midpoint of the cut face....

    [...]

  • ...Following the conservative discretization method in [21], for all cells, i, in which pi is defined,...

    [...]

Journal ArticleDOI
TL;DR: A Cartesian cut-cell method which allows the solution of two- and three-dimensional viscous, compressible flow problems on arbitrarily refined graded meshes is presented and is shown to be second-order accurate in L1.

160 citations

References
More filters
Journal ArticleDOI

40,330 citations


Additional excerpts

  • ...Similar approaches based on formally inconsistent discretizations at the irregular boundary have been used previously and observed to be stable [1, 9], so we expect that the extension to the more accurate boundary discretization should be straightforward....

    [...]

Book
07 Jan 2013
TL;DR: In this article, Leray-Schauder and Harnack this article considered the Dirichlet Problem for Poisson's Equation and showed that it is a special case of Divergence Form Operators.
Abstract: Chapter 1. Introduction Part I: Linear Equations Chapter 2. Laplace's Equation 2.1 The Mean Value Inequalities 2.2 Maximum and Minimum Principle 2.3 The Harnack Inequality 2.4 Green's Representation 2.5 The Poisson Integral 2.6 Convergence Theorems 2.7 Interior Estimates of Derivatives 2.8 The Dirichlet Problem the Method of Subharmonic Functions 2.9 Capacity Problems Chapter 3. The Classical Maximum Principle 3.1 The Weak Maximum Principle 3.2 The Strong Maximum Principle 3.3 Apriori Bounds 3.4 Gradient Estimates for Poisson's Equation 3.5 A Harnack Inequality 3.6 Operators in Divergence Form Notes Problems Chapter 4. Poisson's Equation and Newtonian Potential 4.1 Holder Continuity 4.2 The Dirichlet Problem for Poisson's Equation 4.3 Holder Estimates for the Second Derivatives 4.4 Estimates at the Boundary 4.5 Holder Estimates for the First Derivatives Notes Problems Chapter 5. Banach and Hilbert Spaces 5.1 The Contraction Mapping 5.2 The Method of Cintinuity 5.3 The Fredholm Alternative 5.4 Dual Spaces and Adjoints 5.5 Hilbert Spaces 5.6 The Projection Theorem 5.7 The Riesz Representation Theorem 5.8 The Lax-Milgram Theorem 5.9 The Fredholm Alternative in Hilbert Spaces 5.10 Weak Compactness Notes Problems Chapter 6. Classical Solutions the Schauder Approach 6.1 The Schauder Interior Estimates 6.2 Boundary and Global Estimates 6.3 The Dirichlet Problem 6.4 Interior and Boundary Regularity 6.5 An Alternative Approach 6.6 Non-Uniformly Elliptic Equations 6.7 Other Boundary Conditions the Obliue Derivative Problem 6.8 Appendix 1: Interpolation Inequalities 6.9 Appendix 2: Extension Lemmas Notes Problems Chapter 7. Sobolev Spaces 7.1 L^p spaces 7.2 Regularization and Approximation by Smooth Functions 7.3 Weak Derivatives 7.4 The Chain Rule 7.5 The W^(k,p) Spaces 7.6 DensityTheorems 7.7 Imbedding Theorems 7.8 Potential Estimates and Imbedding Theorems 7.9 The Morrey and John-Nirenberg Estimes 7.10 Compactness Results 7.11 Difference Quotients 7.12 Extension and Interpolation Notes Problems Chapter 8 Generalized Solutions and Regularity 8.1 The Weak Maximum Principle 8.2 Solvability of the Dirichlet Problem 8.3 Diferentiability of Weak Solutions 8.4 Global Regularity 8.5 Global Boundedness of Weak Solutions 8.6 Local Properties of Weak Solutions 8.7 The Strong Maximum Principle 8.8 The Harnack Inequality 8.9 Holder Continuity 8.10 Local Estimates at the Boundary 8.11 Holder Estimates for the First Derivatives 8.12 The Eigenvalue Problem Notes Problems Chapter 9. Strong Solutions 9.1 Maximum Princiles for Strong Solutions 9.2 L^p Estimates: Preliminary Analysis 9.3 The Marcinkiewicz Interpolation Theorem 9.4 The Calderon-Zygmund Inequality 9.5 L^p Estimates 9.6 The Dirichlet Problem 9.7 A Local Maximum Principle 9.8 Holder and Harnack Estimates 9.9 Local Estimates at the Boundary Notes Problems Part II: Quasilinear Equations Chapter 10. Maximum and Comparison Principles 10.1 The Comparison Principle 10.2 Maximum Principles 10.3 A Counterexample 10.4 Comparison Principles for Divergence Form Operators 10.5 Maximum Principles for Divergence Form Operators Notes Problems Chapter 11. Topological Fixed Point Theorems and Their Application 11.1 The Schauder Fixes Point Theorem 11.2 The Leray-Schauder Theorem: a Special Case 11.3 An Application 11.4 The Leray-Schauder Fixed Point Theorem 11.5 Variational Problems Notes Chapter 12. Equations in Two Variables 12.1 Quasiconformal Mappings 12.2 holder Gradient Estimates for Linear Equations 12.3 The Dirichlet Problem for Uniformly Elliptic Equations 12.4 Non-Uniformly Elliptic Equations Notes Problems Chapter 13. Holder Estimates for

18,443 citations

Book ChapterDOI
01 Jan 1997
TL;DR: In this paper, a class of partial differential equations that generalize and are represented by Laplace's equation was studied. And the authors used the notation D i u, D ij u for partial derivatives with respect to x i and x i, x j and the summation convention on repeated indices.
Abstract: We study in this chapter a class of partial differential equations that generalize and are to a large extent represented by Laplace’s equation. These are the elliptic partial differential equations of second order. A linear partial differential operator L defined by $$ Lu{\text{: = }}{a_{ij}}\left( x \right){D_{ij}}u + {b_i}\left( x \right){D_i}u + c\left( x \right)u $$ is elliptic on Ω ⊂ ℝ n if the symmetric matrix [a ij ] is positive definite for each x ∈ Ω. We have used the notation D i u, D ij u for partial derivatives with respect to x i and x i , x j and the summation convention on repeated indices is used. A nonlinear operator Q, $$ Q\left( u \right): = {a_{ij}}\left( {x,u,Du} \right){D_{ij}}u + b\left( {x,u,Du} \right) $$ [D u = (D 1 u, ..., D n u)], is elliptic on a subset of ℝ n × ℝ × ℝ n ] if [a ij (x, u, p)] is positive definite for all (x, u, p) in this set. Operators of this form are called quasilinear. In all of our examples the domain of the coefficients of the operator Q will be Ω × ℝ × ℝ n for Ω a domain in ℝ n . The function u will be in C 2(Ω) unless explicitly stated otherwise.

8,299 citations


"A Cartesian grid embedded boundary ..." refers background in this paper

  • ...However, it is well known that, for any domain with smooth boundary, a smooth function can be extended to all of R with a bound on the relative increase in the C norms that depends only on the domain and (k; ) [5]....

    [...]

Journal ArticleDOI
TL;DR: In this paper, a second-order projection method for the Navier-Stokes equations is proposed, which uses a specialized higher-order Godunov method for differencing the nonlinear convective terms.

1,287 citations


"A Cartesian grid embedded boundary ..." refers methods in this paper

  • ...The method described here, together with that in [6] for elliptic PDEs and [8] for hyperbolic PDEs, provide the fundamental components required for developing second-order accurate methods for a broad range of continuum mechanics problems in irregular geometries based on the predictor–corrector approach in [2]....

    [...]

Journal ArticleDOI
TL;DR: A numerical method for solving Poisson's equation, with variable coefficients and Dirichlet boundary conditions, on two-dimensional regions using a finite-volume discretization, which embeds the domain in a regular Cartesian grid.

470 citations


"A Cartesian grid embedded boundary ..." refers background or methods in this paper

  • ...As in previous work on elliptic problems [6], our approach uses a finite-volume discretization, which embeds the domain in a regular Cartesian grid....

    [...]

  • ...We follow the approach described in [6, 7]....

    [...]

  • ...With Dirichlet boundary conditions as from (3), we compute an estimate of ∂ψ ∂n by interpolating from the grid values and the values at the boundaries; for details, see [6]....

    [...]

  • ...The method described here, together with that in [6] for elliptic PDEs and [8] for hyperbolic PDEs, provide the fundamental components required for developing second-order accurate methods for a broad range of continuum mechanics problems in irregular geometries based on the predictor–corrector approach in [2]....

    [...]

  • ...This is routine for the case in which the embedded boundary is contained in the finest level of refinement [6], but requires some additional discretization design when the embedded boundary crosses coarse–fine interfaces....

    [...]

Frequently Asked Questions (1)
Q1. What are the contributions mentioned in the paper "A cartesian grid embedded boundary method for the heat equation on irregular domains" ?

The authors present an algorithm for solving the heat equation on irregular time-dependent domains.